Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Myc-dependent role for cohesin in the heterokaryon-mediated reprogramming of somatic nuclei

ABSTRACT: Analysis of gene expression changes in mESCs where the cohesin subunit Scc1 has been depleted. There are 6 samples. 3 Scc1 wt/wt ERT2-Cre biological replicas and 3 Scc1 lox/lox ERT2-Cre biological replicas, all treated with 4'-OHT 80nM final concentration for 24h.

ORGANISM(S): Mus musculus

PROVIDER: GSE62325 | GEO | 2015/02/19

SECONDARY ACCESSION(S): PRJNA263831

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A Myc-dependent role for cohesin in the heterokaryon-mediated reprogramming of somatic nuclei

Project description:Analysis of gene expression changes in mESCs where the cohesin subunit Scc1 has been depleted. There are 6 samples. 3 Scc1 wt/wt ERT2-Cre biological replicas and 3 Scc1 lox/lox ERT2-Cre biological replicas, all treated with 4'-OHT 80nM final concentration for 24h. Scc1 wt/wt and Scc1 lox/lox ERT2-Cre mES cells where grown in N2B27 +2i+LIF medium (Ying et al. 2008) for 24h in the presence of 80mM 4-OHT to induce cohesin depletion. Three biological replicates were collected and RNA was extracted. Microarray samples were prepared following the manufacturers instructions (Affymetrix) using 200ng of total RNA. Microarry samples were hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST Arrays and the analysis was performed using the Bioconductor Package for R.

2015-02-19 | E-GEOD-62325 | biostudies-arrayexpress

BMP7 Signaling in TGFb Receptor-2 deficient Stromal Cells Provokes Epithelial Carcinogenesis

Project description:Mouse forestomach fibroblasts were isolated from a wild-type (wt), a FSP-Cre;TGFBR2 lox/lox (TGFBR2cKO) mouse, and a FSP-Cre;TGFBR2 lox/lox; Smad4 lox/lox (TGFBR2/SMAD4 cKO) mouse and expanded in vitro. The cells were then harvested and processed for RNA purification. While wt and TGFBR2/SMAD4 cKO mice are healthy, the TGFBR2cKO mouse presents with forestomach cancer.

2020-11-01 | GSE106442 | GEO

Cre-ERT mediated antiviral induction

2016-05-18 | GSE72024 | GEO

The Aurora B kinase and the polycomb protein Ring1B combine to regulate active promoters in quiescent lymphocytes [ChIP-seq]

Project description:Genome-wide distribution of proteins and histone marks in CD43 negative mouse resting B cells ChIP-seq analyses of Aurora B, Ring1B, Bcx7, USP16, H3K27me3, and Ezh2 were carried out on wild-typeCD43 negative resting B cells. ChIP-seq datasets obtained from Aurora B knockout and RingiB knockout cells were used as negative controls to validate the signals for Aurora B and Ring1B from wild-type cells. 8WG16 ChIP-seq datasets were generated from WT (Cre-ERt2 homozygous) and Ring1B KO (Cre-ERt2/Rnf2 flox homozygous). RNAP-S5ph ChIP-seq datasets were generated from WT (Cre-ERt2 homozygous) and Aurkb KO (Cre-ERt2/Aurkb flox homozygous). ChIP-seq analyses of H3S28 phosphorylation (H3S28ph) and H2AK119 monoubiquitination (H2Aub1) in wild-type (Cre-ERt2 homozygous) and Aurora B KO (Cre-ERt2/Aurkb flox homozygous) CD43 negative resting B cells treated with 250nM tamoxifen (4-hydroxytamoxifen) for 48 hours. ChIP-seq analyses of the levels of unphosphorylated RNA Pol II (8WG16) and serine 5-phosphorylated RNA Pol II (RNAP-S5ph) were conducted in Aurkb KO (Cre-ERt2/Aurkb flox homozygous) and Ring1B KO (Cre-ERt2/Rnf2 flox homozygous) CD43 negative resting B cells treated with 250nM tamoxifen (4-hydroxytamoxifen) for 48 hours respectively). All libraries were prepared from sonicated, formaldehyde-crossilinked chromatin. For H2Aub1, ChIP was performed using micrococcal nuclease-digested, unfixed chromatin, instead.

2013-09-27 | E-GEOD-42705 | biostudies-arrayexpress

RNA sequencing of inguinal white adipose tissue from seipin-deficient mice and appropriate controls

Project description:We generated Bscl2lox/lox mice X ERT2-Adipoq-CRE mice, allowing inducible seipin deletion in adipocytes upon tamoxifen addition (iATSKO). Indeed, a 5-day tamoxifen treatment led to a dramatic decrease in Bscl2 mRNA in the adipose tissue. To study the effects of seipin deficiency in vivo on adipose tissue homeostasis in an unbiased manner, we used 3’-signal recognition particle (SRP) RNA sequencing.

2022-01-11 | GSE188544 | GEO

TGFbRII-Eomes in CD4 T cells during chronic viral infection

Project description:Transcriptome analysis of CD4+ PD1+ T cells during LCMV CL13 infection Gene expression in WT and ERt2-cre;TGFbRII flox virus specific CD4 T cells

2016-06-30 | GSE83921 | GEO

Effect of Tet2 deletion on gene expression in mice

Project description:To investigate the effect of Tet2 on gene expression, we established Nestin Cre+ Tet2lox/lox (Tet2 cKO) mice and Nestin Cre- Tet2lox/lox (WT) mice , collected their habenular tissue, and compared the differential gene expressions at mRNA levels. We then performed gene expression profiling analysis using data obtained from RNA-seq in the habenular of 2-month mice.

2023-05-24 | GSE232920 | GEO

Cre-ERT mediated antiviral induction

Project description:In this work, we aimed at studying the impact of microRNAs on antiviral responses, using inducible deletion of one or two copies of Dicer1 (in Dicer-floxed x EsrCRE+ MEFs). Unexpectedly, we discovered that Cre-ERT activation by hydroxytamoxifen (OHT) alone, independent of Dicer1 deletion, had a strong impact on antiviral responses. These microarrays were performed on SV40 immortalized Dicer1 fl/fl EsrCRE+ MEFs, Dicer1 fl/wt EsrCRE+ MEFs, 96 h after initial OHT treatment, and SV40 immortalized Dicer1 wt/wt EsrCRE+ MEFs, Dicer1 wt/wt EsrCRE-neg MEFs (Wild Type MEFs), 48 h after initial OHT treatment. These analyses revealed the strong induction of several antiviral genes (Rsad2, Cxcl10...), following Cre-ERT activation. SV40 immortalized mouse embryonic fibroblasts from various genotypes were stimulated 24h with 500nM hydroxytamoxifen, and further expanded for 24 or 72h. Each sample was analyzed on Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray Each sample is in simplicate - no biological replicates; sample 1-4 were processed/analyzed on a different microarray slide to 5-8 (different day/operator)

2016-05-18 | E-GEOD-72024 | biostudies-arrayexpress

Mouse retina from Msi1/Msi2 double knockout in photoreceptor cells

Project description:This quantitative protepomics study (TMT10 isobaric labeling) of the protein expression in the retina of Msi1/Msi2 double knockout mouse compared to floxed controls. The Msi1 and Msi2 genes were knocked out in photoreceptor cells using tamoxifen inducible Cre (Cre-ERT2) under the control of Pde6g promoter. Tamoxifen was administered by intrapertoneal injection for three consecutive day starting at postnatald day 30, and the retina was collected at postnatal day 51. Retinas from floxed animals lacking the Cre recombinase and treated with tamoxifen were used as controls. Five biological replicates for each knockout (three femailes, two males) and control (two femaes and three males) group were used.

2022-03-10 | PXD030748 | Pride

Effect of PCGF6 loss of function in intestinal adult epithelial cells [RNA-seq]

Project description:We generated RNAseq expression analyses of PCGF6 WT and KO intestinal crypts in two independent replicates using two distinct transgenic models (AhCre and Villin Cre-ERT2) We then performed differential expression analyses of PCGF6 KO vs. WT independently in the AhCre and Villin transgenic models

2023-12-18 | GSE228479 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data